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Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
The hysteretic behavior exhibited by collagen fibrils, when subjected to cyclic loading, is known to result in both dissipation as well as accumulation of residual strain. On subsequent relaxation, partial recovery has also been reported.…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
The early planetesimal growth proceeds through a sequence of sticking collisions of dust agglomerates. Very uncertain is still the relative velocity regime in which growth rather than destruction can take place. The outcome of a collision…
We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving…
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively…
We present an equation-free computational approach to the study of the coarse-grained dynamics of {\it finite} assemblies of {\it non-identical} coupled oscillators at and near full synchronization. We use coarse-grained observables which…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
The bottleneck in enhanced sampling lies in finding collective variables (CVs) that can effectively accelerate protein conformational changes. True reaction coordinates (tRCs) that can predict the committor are considered the optimal CVs,…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
In this work, we apply phase field simulations to examine the coarsening behavior of morphologically complex two-phase microstructures in which the phases have highly dissimilar mobilities, a condition approaching that found in experimental…
In a recent publication we established an analogy between the free energy of a hard sphere system and the energy of an elastic network [1]. This result enables one to study the free energy landscape of hard spheres, in particular to define…
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…